The aircraft was hijacked by gunmen shortly after it entered Indian airspace at about 17:30 IST. Hijackers ordered the aircraft to be flown to several locations. After touching down in Amritsar, Lahore, and Dubai, the hijackers finally forced the aircraft to land in Kandahar, Afghanistan, which at the time was controlled by the Taliban. The hijackers released 27 of 176 passengers in Dubai but fatally stabbed one and wounded several others.

At that time, most of Afghanistan, including Kandahar where the plane landed, was under Taliban control. Initially it was thought that Taliban was on Indian side but later it became apparent that they are working in collaboration with ISI. Taliban fighters surrounded the aircraft to prevent any Indian military intervention,[4][5] which was found by current National Security Advisor Ajit Doval when he landed there and they also found two ISI men were on the tarmac and others soon joined them in which one was a lieutenant colonel and the other a major. Doval said that if the Taliban hijackers did not have ISI support, India could have resolved the crisis.[3]

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Anil Sharma, the chief flight attendant on IC-814, later recalled that a masked, bespectacled man threatened to blow up the plane with a bomb and ordered Captain Devi Sharan to "fly west".[10] Four other men wearing red masks then stood up and took positions throughout the aircraft. The hijackers wanted Captain Sharan to divert the aircraft over Lucknow and head towards Lahore. However, due to insufficient fuel, Captain Sharan told the hijackers that they had to land in Amritsar, India.[10]

At Amritsar, Captain requested refuelling for the aircraft. The aircraft stood there for more than 45 minutes but no credible efforts were made to rescue the passengers and instead confusion was spread.[11] However, the Crisis Management Group in Delhi directed Amritsar Airport authorities to ensure that the plane was immobilised. The armed personnel of the Punjab police were already in position to try and do this. They did not receive approval from New Delhi. Eventually, a fuel tanker was dispatched and instructed to block the approach of the aircraft. As the tanker sped towards the aircraft, air traffic control radioed the pilot to slow down, and the tanker immediately came to a stop. This sudden stop aroused the hijackers' suspicion and they forced the aircraft to take off immediately, without clearance from air traffic control. The aircraft missed the tanker by only a few feet.[12]

Later, it was revealed that there were efforts by ex-RAW chief AS Daulat and others to cover up the real motives of why the plane was not immobilised and why there were no commando-operation to neutralise the threat. The RAW officer named Shashi Bhushan Singh Tomar, husband of Sonia Tomar, was boarded on the plane, who was a brother-in-law of N K Singh, secretary to then Prime Minister Atal Bihari Vajpayee and he ensured that the plane would be let off and no commando operation would be carried out to ensure his brother-in-law's safety.[13] According to RAW officer, R K Yadav, author of Mission R&AW, days before the hijacking, UV Singh, another RAW operative in Kathmandu informed Tomar that Pakistani terrorists were planning to hijack an Indian plane and he ordered Singh to check the veracity of his report where Singh vouched for its reliability but Tomar rebuked him and told him not to spread rumours. Later, Tomar was found on the same plane which was hijacked and became the cause of failure of the operation.[13] The then Prime Minister Atal Bihari Vajpayee was kept in the dark until around 7:00 pm, a full hour and 40 minutes since the hijacking of IC 814 and he came to know about the hijacking only after disembarking from the aircraft in the VIP bay of Palam Technical Area.[11]

Due to extremely low fuel level, the aircraft requested an emergency landing in Lahore, Pakistan. Pakistan initially denied the request. Pakistan briefly also switched off all lights at Lahore Airport.[14] On understanding that the only other option for the aircraft was to crash land, Lahore Airport switched on its lights and allowed the aircraft to land. India made two requests to Pakistan soon after the hijacked plane landed in Lahore; first to ensure the plane did not leave Lahore and second that Indian High Commissioner G. Parthasarathy in Islamabad be given a helicopter to reach Lahore as soon as possible, but the helicopter was provided when the hijacked airplane already left Lahore after Lahore airport officials refuelled the aircraft, got their commandos to surround the plane and allowed it to leave Lahore at 22:32 IST.[14] The plane was there for two and half hours and Pakistani officials rejected the pilot's request to offload some women and children passengers due to tense relations with India.[15] The senior Foreign Office officials were told by Pakistanis that there were reports from the pilot that the hijackers had killed passengers on board which were found to be false later.[14]

The aircraft took off for Dubai where 27 passengers aboard the flight were released.[15] The hijackers also released a critically injured 25-year-old male hostage, Rupan Katyal, who was stabbed by the hijackers multiple times. Rupan had died before the aircraft landed in Al Minhad Air Base, in Dubai. Indian authorities wanted Indian commandos trained in hijack rescue to assault the aircraft but the UAE government refused permission.[16]

After the aircraft landed in Kandahar, Taliban authorities offered to mediate between India and the hijackers, which India believed initially. Since India did not recognise the Taliban regime, it dispatched an official from its High Commission in Islamabad to Kandahar.[15] India's lack of previous contact with the Taliban regime complicated the negotiating process.[17][18]

However, the intention of the Taliban was under doubt after its armed fighters surrounded the aircraft.[19] The Taliban maintained that the forces were deployed in an attempt to dissuade the hijackers from killing or injuring the hostages but some analysts believe it was done to prevent an Indian military operation against the hijackers.[5][4]IB chief Ajit Doval claimed that the hijackers were getting active ISI support in Kandahar and that the ISI had removed all the pressure the Indians were trying to put on the hijackers and even that their safe exit was guaranteed, so they had no need to negotiate an escape route. Doval also mentioned that if the hijackers were not getting active ISI support in Kandahar then India could have resolved the hijacking.[3]

After the three militants landed in Kandahar, the hostages aboard the aircraft were freed. On 31 December 1999, the freed hostages of Indian Airlines Flight 814 were flown back through special plane.[citation needed]

Meanwhile, the Taliban had given the hijackers ten hours to leave Afghanistan. The five hijackers departed with a Taliban hostage to ensure their safe passage and were reported to have left Afghanistan.[citation needed]

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The incident is seen as a failure of the BJP government under Prime Minister Atal Bihari Vajpayee and IB chief Ajit Doval said that India would have had a stronger negotiating hand if the aircraft had not been allowed to leave Indian territory.[26][27] Doval, the IB chief, who led the four-member negotiating team to Kandahar, described the whole incident as a "diplomatic failure" of the government in their inability to make the US and UAE use their influence to help secure a quick release of the passengers.[28]

The case was investigated by Central Bureau of Investigation (CBI), which charged 10 people out of whom seven including the five hijackers were still absconding and are in Pakistan.[29][failed verification] On 5 Feb 2008, a special anti-hijacking Patiala House Court sentenced all three accused, namely Abdul Latif, Yusuf Nepali and Dilip Kumar Bhujel, to life imprisonment. They were charged with helping the hijackers in procuring fake passports and taking weapons on board.[30] However, CBI moved Punjab and Haryana High Court demanding the death penalty (instead of life imprisonment) for Abdul Latif.[29] The case came up for regular hearing in high court in September 2012,[31] but the CBI's application was rejected. Also, Abdul Latif's application for parole was rejected in 2015.[32] On 13 September 2012, the Jammu and Kashmir Police arrested terror suspect Mehrajuddin Dand, who allegedly provided logistical support for the hijacking of IC-814 in 1999. He allegedly provided travel papers to the hijackers.[33]

Captain Devi Sharan (Commander of IC814) recounted the events in a book titled Flight into Fear – A Captain's Story (2000).
The book was written in collaboration with journalist Srinjoy Chowdhury.

Flight Engineer Anil K. Jaggia also wrote a book specifically depicting the events that unfolded during the hijacking ordeal. His book is titled IC 814 Hijacked! The Inside Story. The book was written in collaboration with Saurabh Shukla.

The aircraft was returned to Indian Airlines in January 2000 and continued to be operated until May 2002, before it was bought by Airbus. It was then stored at Chhatrapati Shivaji Maharaj International Airport in March 2003, and then it was scrapped there in December 2003.[34]

In November 2018, retired Air Marshal, Air Marshal S Y Sarur, has narrate dilemma of officials during the Kandahar hijacking in 1999, as journalist Barkha dutt had threatened to get him fired her team weren't allowed in the Tech area for reporting, which was a sensitive area at the time of the hijacking.[35]